Sequence
atgc intronic sequence ATGC exonic sequencegtataaattactcttcacattactatagttctcgtaattgtattggttccatctgtttgataatataatgttatttgattagGTAAGCATTGTTATGGAGCAAATGATGCGATTGCTCCACTATTGTGGTTTACCCGCTGAAGATGTGGACTTTATAAATTCTGATGGGAAGACAATGAACA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G62530.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G62530.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA05G01300.2 (Glycine max), 3'ss of exon 8
-------gtataaattactcttcacattactatagttc----tcgtaattgtattggttccatctgtttgataatataatgtt------atttgat-tagGTAAGCATTGTTATGGAGCAAATGATGCGATTGCTCCACTATTGTGGTTTACCCGCTGAAGATGTGGACTTTATAAATTCTGATGGGAAGACAATGAACA
||| | | | |||||| | | || | |||| | | ||| | | || | | | || | || || ||||| |||||||||||||| |||||| |||| |||| || ||||| ||||| || |||||||| ||||| ||||||||||||||||||||||||||||
ttttcatctatcagattttggaaacattaattttatttgcctttaaaattcaaatctttcagcaattataattctgaattattgactcaaattaatgtagGTGAGCATTGTTATGGAACAAATGTTGCGCCTGCTTCATACCTGTGGCTTACCTGCAGAAGATGTAGACTTCATAAATTCTGATGGGAAGACAATGAACA
upper sequence: AT5G62530.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA05G01290.1 (Glycine max), 3'ss of exon 7
--------------------gtataaattactcttcacattactatagttctcgtaattgtattggttccatctgtttgataatataatgttatttgattagGTAAGCATTGTTATGGAGCAAATGATGCGATTGCTCCACTATTGTGGTTTACCCGCTGAAGATGTGGACTTTATAAATTCTGATGGGAAGACAATGAACA
| | | | | | || | | | ||| | || || | | | || | | | || | | ||| ||||| |||||||||||||| |||||| |||| |||| || | ||||||||||| |||||||| ||||| ||||||||||| ||||||||||||||||
ctcttcatctattggattttggacatgtgaattttatttgtttttaaattcaaatctttctacagttacaat--gctgaaccatcgactcaaattgttgtagGTGAGCATTGTTATGGACCAAATGTTGCGCCTGCTTCATAACTGTGGTTTACCTCTAGAAGATGTAGACTTCATAAATTCTGACGGGAAGACAATGAACA
upper sequence: AT5G62530.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA17G10610.1 (Glycine max), 3'ss of exon 8
------------------gtataaattactcttcacattactatagttctcgtaattgtattggttccatctgtttgataatataatgttatttgattagGTAAGCATTGTTATGGAGCAAATGATGCGATTGCTCCACTATTGTGGTTTACCCGCTGAAGATGTGGACTTTATAAATTCTGATGGGAAGACAATGAACA
| |||| ||| || |||| || | | | | | || | || || | | ||| ||||| |||||||||||||| |||||| |||| |||| || ||||| ||||| |||||||| ||||| ||||||||||||||||||||||||||||
ttcttcatctattggattttggaaatgtgacttttatttgctattaaattcaaatctttctgcagtgacaatgctgaattattgactcaaattgttgtagGTGAGCATTGTTATGGAACAAATGTTGCGCCTGCTTCATACCTGTGGCTTACCTCTAGAAGATGTAGACTTCATAAATTCTGATGGGAAGACAATGAACA
upper sequence: AT5G62530.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv17s0000g05800.t01 (Vitis vinifera), 3'ss of exon 8
-------------gtataaattactcttcacattac-tatagttctcgtaat----tgtattggttccatc-tgtttgataatataatgttatttgattagGTAAGCATTGTTATGGAGCAAATGATGCGATTGCTCCACTATTGTGGTTTACCCGCTGAAGATGTGGACTTTATAAATTCTGATGGGAAGACAATGAACA
||| | || || ||||| || || | ||| | ||| ||| | | | ||| || | || ||| |||||| || |||||||||||||| ||||| |||||||| || ||||||| || || || ||| | |||||||||||||||||||| |||||||||||||
ttactaagacactctatttctatctttttccattagacattcttattaaaatattttatatgcagattatcatatatactaac-tattttttttttcttagGTGAGTATTGTTATGGAGCAGATGATTCGATTGCTTCATCATTGTGGGTTGCCTATGGAGGATCTTGACTTTATAAATTCTGATGGAAAGACAATGAACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttctcgtaattgtattggttccatctgtttgataatataatgttatttgattagGTAAGCATTGTTATGGAGCAAATGATGCGATTGCTCCACTATTGTGGTTTACCCGCTGAAGATGTGGACTTTATAAATTCTGATGGGAAGACAATGAACA
gtttgat putative branch site (score: 5)
tgtttgataatataat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataaattactcttcacattactatagttctcgtaattgtattggttccatctgtttgataatataatgttatttgattagGTAAGCATTGTTATGGAGCAAATGATGCGATTGCTCCACTATTGTGGTTTACCCGCTGAAGATGTGGACTTTATAAATTCTGATGGGAAGACAATGAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA